Tom Conn of Inside Spanish Football had earlier highlighted a report in AS:

According to Spanish sports daily, AS, Cristiano does not want to miss the slightest bit of rehab on his knee, as he continues his fitness race ahead of next week’s Champions League semi-final tie against Bayern Munich and will therefore stay behind while the rest of the team travels to Valencia and will arrive shortly before the game on Wednesday, after his morning treatment.

Real Madrid will take the high-speed AVE train to Valencia right after Tuesday’s training session and Cristiano, along with Arbeloa, Marcelo, Khedira and maybe even Jesé will all take a chartered plane to to Valencia to support their teammates in their attempt to win their first title of the season.

Update from Friday, April 11

Carlo Ancelotti has confirmed Cristiano Ronaldo has a thigh injury, but is unsure if he will miss the midweek Copa del Rey final, per Real Madrid's official Twitter:

Cristiano Ronaldo will reportedly miss Real Madrid's Copa del Rey final against Barcelona at Valencia's Mestalla Stadium on Wednesday after picking up a thigh injury that could see him out of action for over two weeks.

The news was reported by Spanish newspaper AS via its Twitter feed:

BREAKING: Cristiano will miss Wednesday's Copa del Rey final after suffering a thigh muscle tear. He faces 15 days on the sidelines.

It comes just two days after Carlo Ancelotti's side reached the semi-finals of the Champions League thanks to a 3-2 aggregate victory over Borussia Dortmund. On Wednesday, Ronaldo boasted his club's success: